JAL-2119 fixes for broken links in help files

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 545f0c1..744370b 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -110,7 +110,7 @@
     followed by a <em>description</em> for the row, which is shown in a
     tooltip when the user mouses over the annotation row's label. Since
     Jalview 2.7, the description field may also contain HTML tags (in
-    the same way as a <a href="featuresFile.html">sequence feature's</a>
+    the same way as a <a href="featuresFormat.html">sequence feature's</a>
     label), providing the text is enclosed in an &lt;html/&gt; tag.
   <ul>
     <em>Please note: URL links embedded in HTML descriptions are

diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index ed5bef3..1c36abd 100644 (file)
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -53,7 +53,7 @@
     <li>On selecting rows, columns or regions in one alignment, the
       corresponding selection is made in the other</li>
     <li>Sequence ordering in one alignment (using the cursor, or <strong><a
-        href="../calculate/sorting.html"
+        href="../calculations/sorting.html"
       >"Calculate&#8594;Sort")</a></strong> is also applied to the other
     </li>
     <li>Editing (gap insertion / deletion) in the protein alignment
@@ -75,7 +75,7 @@
       panels.</li>
     <li>Panel heights are adjusted dragging the divider between
       them using the mouse</li>
-    <li><a href="menus/alwview.html"><strong>"View&#8594;New
+    <li><a href="../menus/alwview.html"><strong>"View&#8594;New
           View / Expand Views / Gather Views"</strong></a> behave as for a normal
       alignment window, but always create new views as Split Frames</li>
   </ul>

diff --git a/help/html/keys.html b/help/html/keys.html
index a477457..f129551 100755 (executable)
--- a/help/html/keys.html
+++ b/help/html/keys.html
@@ -159,7 +159,7 @@
       <td>Both</td>
       <td>Cuts the (fully) selected sequences from the alignment. <!-- not yet in this version 
 This will not happen if only some
-columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
+columns are selected, you should use the <a href="features/hiddenRegions.html">Hide Regions feature</a> instead.-->
       </td>
     </tr>
     <tr>

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 1eb2366..353fb41 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -144,9 +144,8 @@
             and sequence description to be entered. Press OK to accept
             your edit. To save sequence descriptions, you must save in
             Fasta, PIR or Jalview File format.</em></li>
-        <li><a href="sqaddrefannot"><strong>Add
-              Reference Annotations<br>
-          </strong><em>When enabled, copies any available alignment
+        <li><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
+              <em>When enabled, copies any available alignment
               annotation for this sequence to the current view.</em></li>
         <li><strong>Set as Reference</strong> or <strong>Unmark
             as Reference</strong><br /> Sets or unsets the reference sequence for

diff --git a/help/html/releases.html b/help/html/releases.html
index 0bb5fb7..d4bbd33 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1392,10 +1392,7 @@
             between different screens.</li>
           <li>New preference items for sequence ID tooltip and
             consensus annotation</li>
-          <li>Client to submit sequences and IDs to <a
-            href="webServices/index.html#envision2">Envision2</a>
-            Workflows
-          </li>
+          <li>Client to submit sequences and IDs to Envision2 Workflows</li>
           <li><em>Vamsas Capabilities</em>
             <ul>
               <li>Improved VAMSAS synchronization (Jalview archive

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 04ccd8f..b03bb9d 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -88,7 +88,7 @@
     >REST</a> web services exposing sequence alignment, analysis, and
     secondary structure prediction programs. Originally, Jalview 2's
     services were maintained by the Barton group at the University of
-    Dundee, and ran programs on the Life Sciences High-performace
+    Dundee, and ran programs on the Life Sciences High-performance
     Computing Cluster. With the advent of <a
       href="http://www.compbio.dundee.ac.uk/JABAWS"
     >JABAWS</a>, however, it is possible for anyone to host Jalview web

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index de0f8cd..7a23d58 100644 (file)
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -83,7 +83,7 @@
     <em>Please Note:
       <ul>
         <li>The regular expressions supported by Jalview are those
-          provided by the <a href="www.javaregex.com">Stevesoft
+          provided by the <a href="http://www.javaregex.com">Stevesoft
             javaregex package</a>.
         </li>
         <li>Some characters must be escaped when specifying them as